Contacts of the helix formed by residues 86 - 101 (chain B) in PDB entry 3A3K
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with CYS 86 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B TYR* 3.9 5.8 - - - -
18B TRP* 3.3 30.2 - - - +
60B CYS* 2.1 51.6 - - + -
85B GLY* 1.3 77.9 - - - +
87B VAL* 1.3 60.3 + - - +
88B TYR* 5.5 0.2 - - + -
89B SER* 3.7 14.7 - - - +
90B ALA* 2.9 29.8 + - - +
109B ALA* 4.9 0.2 - - - -
161B ASP* 3.3 17.3 - - - +
601B BR 3.4 1.4 - - + +
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Residues in contact with VAL 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B GLY 3.5 1.0 + - - -
86B CYS* 1.3 70.7 - - - +
88B TYR* 1.3 66.6 + - + +
90B ALA* 4.2 0.3 - - - +
91B ALA* 3.2 26.0 + - + +
109B ALA* 4.3 8.7 - - - +
110B PRO* 3.9 24.2 - - + -
111B ALA* 3.6 31.6 - - + +
114B ILE* 4.7 6.8 - - + +
161B ASP* 3.1 18.4 + - - +
166B PHE* 3.5 41.5 - - + -
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Residues in contact with TYR 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B CYS* 5.9 2.7 - - - +
61B SER 5.4 0.7 - - - -
62B ASP* 3.3 33.2 - - + +
86B CYS* 3.3 1.3 - - + -
87B VAL* 1.3 82.6 - - + +
89B SER* 1.3 57.7 + - - +
91B ALA* 4.4 3.3 - - + +
92B PRO* 3.1 21.8 - - - +
160B ASP 4.1 19.3 - - - -
161B ASP* 3.5 16.3 + - - +
162B ARG* 3.5 34.6 + - - -
165B PHE* 5.5 0.2 - - - -
166B PHE* 3.7 29.9 - + - -
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Residues in contact with SER 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B SER* 3.8 6.2 - - - -
60B CYS* 4.0 4.5 - - - +
61B SER 2.8 37.6 + - - -
62B ASP* 4.5 0.4 - - - +
65B ALA* 3.6 10.8 - - - +
84B PRO* 3.6 20.6 - - - -
86B CYS* 3.3 14.0 + - - +
87B VAL 3.3 0.2 - - - -
88B TYR* 1.3 78.3 - - - +
90B ALA* 1.3 63.0 + - - +
92B PRO* 3.2 16.3 - - - +
93B VAL* 3.4 14.9 - - - +
601B BR 4.3 2.7 - - - -
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Residues in contact with ALA 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B PRO* 3.8 27.8 - - + +
86B CYS 2.9 17.8 + - - +
87B VAL 4.2 1.6 - - - +
89B SER* 1.3 75.9 - - - +
91B ALA* 1.3 58.1 + - - +
94B GLY* 2.7 33.6 + - - -
104B LEU* 5.1 4.5 - - + +
106B THR* 5.7 1.6 - - + -
109B ALA* 3.8 24.2 - - + -
114B ILE* 4.6 5.8 - - + -
120B TYR* 4.2 1.6 - - - -
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Residues in contact with ALA 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B VAL* 3.2 17.3 + - + +
88B TYR* 4.4 4.5 - - + +
90B ALA* 1.3 78.4 - - - +
92B PRO* 1.4 72.1 - - + +
95B ARG* 3.3 8.7 + - - +
114B ILE* 4.0 9.7 - - + +
120B TYR* 3.1 40.1 + - - +
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Residues in contact with PRO 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ASP* 3.4 25.1 - - + +
66B PRO* 4.0 18.2 - - + -
88B TYR 3.1 24.2 - - - +
89B SER 3.2 14.8 - - - +
91B ALA* 1.4 84.2 - - + +
93B VAL* 1.3 59.4 + - - +
95B ARG* 3.2 15.6 + - + +
96B PHE* 3.3 23.6 + - + -
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Residues in contact with VAL 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B VAL* 4.7 2.5 - - + -
65B ALA* 3.7 9.0 - - + +
66B PRO* 3.6 28.7 - - + -
69B ALA* 4.0 17.7 - - + -
81B PHE* 4.8 5.8 - - + -
84B PRO* 3.8 31.9 - - + -
89B SER 3.4 17.7 + - - +
90B ALA 3.4 1.5 + - - +
91B ALA 3.4 0.4 - - - -
92B PRO* 1.3 75.9 - - - +
94B GLY* 1.3 58.1 + - - +
96B PHE* 3.2 11.2 + - - +
97B THR* 3.0 32.2 + - + +
104B LEU* 3.9 11.2 - - + -
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Residues in contact with GLY 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B ALA 2.7 22.4 + - - -
93B VAL* 1.3 75.0 - - - +
95B ARG* 1.3 59.7 + - - +
97B THR* 3.1 20.1 + - - -
98B ALA* 3.2 15.4 + - - +
104B LEU* 4.1 9.6 - - - +
120B TYR* 3.7 22.3 - - - -
121B ALA 4.9 0.2 - - - +
123B THR* 4.6 4.4 + - - -
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Residues in contact with ARG 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ALA 3.3 13.3 + - - +
92B PRO* 3.2 10.1 + - + +
94B GLY* 1.3 75.3 - - - +
96B PHE* 1.3 63.7 + - + +
98B ALA* 3.8 3.6 - - - +
99B HIS* 3.2 22.7 + - - +
119B GLU* 3.6 54.2 + - - +
120B TYR* 3.9 15.7 + - + +
508B SO4 2.9 41.8 + - - -
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Residues in contact with PHE 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B PRO* 4.0 23.8 - - + -
69B ALA* 5.6 1.3 - - + -
70B VAL* 3.8 20.0 - - + -
92B PRO* 3.3 27.4 + - + -
93B VAL* 3.2 11.1 + - + +
95B ARG* 1.3 76.2 - - + +
97B THR* 1.3 60.2 + - - +
99B HIS* 3.1 11.0 + + - +
100B TRP* 2.8 71.5 + + + -
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Residues in contact with THR 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B PHE* 3.8 36.1 - - + -
93B VAL* 3.0 17.1 + - + +
94B GLY* 3.1 18.7 + - - -
96B PHE* 1.3 74.0 - - - +
98B ALA* 1.3 56.8 + - - +
100B TRP* 3.4 17.3 + - + -
101B ARG 3.0 5.9 + - - -
102B VAL* 2.9 46.3 + - + +
104B LEU* 3.6 21.8 - - + +
121B ALA 4.9 1.6 + - - -
123B THR* 4.7 1.7 + - - -
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Residues in contact with ALA 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B GLY 3.2 14.3 + - - +
95B ARG* 3.8 5.4 - - - +
97B THR* 1.3 79.8 + - - +
99B HIS* 1.3 63.6 + - - +
101B ARG* 3.2 17.9 + - - +
119B GLU 3.4 23.3 - - - +
121B ALA* 3.6 33.8 + - + +
122B LEU* 5.2 1.2 - - - +
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Residues in contact with HIS 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B ARG 3.2 11.7 + - - +
96B PHE* 3.1 14.3 + + + +
98B ALA* 1.3 79.0 - - - +
100B TRP* 1.3 80.2 + + - +
101B ARG* 3.4 9.2 + - - +
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Residues in contact with TRP 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B ALA* 3.9 12.6 - - + -
70B VAL* 4.0 18.8 - - + -
73B LYS* 3.5 53.6 + - + +
81B PHE* 3.7 25.1 - + - -
96B PHE* 2.8 58.2 + + + +
97B THR* 3.8 16.8 - - + +
98B ALA 3.3 0.2 - - - -
99B HIS* 1.3 90.7 - + - +
101B ARG* 1.3 70.7 + - - +
102B VAL* 4.0 16.5 - - + +
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Residues in contact with ARG 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B THR 3.0 5.0 + - - -
98B ALA 3.2 13.4 + - - +
99B HIS 4.2 7.0 - - - +
100B TRP* 1.3 81.9 - - - +
102B VAL* 1.3 60.0 + - - +
103B PRO* 4.1 3.5 - - - +
122B LEU* 3.3 20.0 - - - +
343B THR 4.6 4.7 - - - +
345B GLY* 4.2 9.7 + - - -
346B GLU* 2.9 45.6 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il